Locus 4170

Sequence ID	2L_DroMel_CAF1
Location	11,966,473 – 11,966,686
Length	213
Max. P	0.744314

overview

Window 8

Location	11,966,473 – 11,966,586
Length	113
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	92.47
Mean single sequence MFE	-38.04
Consensus MFE	-33.94
Energy contribution	-33.46
Covariance contribution	-0.48
Combinations/Pair	1.17
Mean z-score	-1.14
Structure conservation index	0.89
SVM decision value	-0.02
SVM RNA-class probability	0.522163
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11966473 113 - 22407834
GGAGCUGGCUCAAUUGAUGCUGACAGCGAAUGAAAGGCUCUGGCUGAGAGUCUGCAACUGAGACCACGGCCAGAACGGCAAAGCCCUGGGCACAGUGGUUGAAAAACGAUUUG---
...(((((((((.....(((((...((.........))((((((((.(.((((.......))))).)))))))).)))))......))))).)))).(((....)))......--- ( -37.20)
>DroSec_CAF1 185887 113 - 1
GGAGCUGGCUCAAUUGAUGCUGACAGCGAAUGAAAGGCUCUGGCUGAAAGUCUGCAACUGAGACCUCGGCCAGAAUGGCACAGCCCUGGGCACAGUGGUUGAAAAACGAUUUG---
.(((....)))(((((.((((....((.........))(((((((((..((((.......)))).)))))))))..))))((((((((....))).))))).....)))))..--- ( -36.90)
>DroSim_CAF1 152223 116 - 1
GGAGCUGGCUCAAUUGAUGCUGACAGCGAAUGAAAGGCUCUGGCUGAGAGUCUGCAACUGAGACCUCGGCCAGAACGGCACAGCCCUGGACACAGUGGUUGAAAAACGAUUUGGUU
......((((.(((((.(((((...((.........))((((((((((.((((.......)))))))))))))).)))))((((((((....))).))))).....))))).)))) ( -44.40)
>DroEre_CAF1 160551 113 - 1
GGAGCUGGCUCAAUUGAUGCUGACAGCGAAUGAAAGGCUGUGGCUGAGAGUCUGCAACUGGGACCAUGGCCAGAACAGUGCAGCCCUGGGCACAGUGGUUGAAAAGCGAUUGG---
...(((((((..((((.(((.....))).......((((((((((.((.........)).)).))))))))....))))..))))...))).((((.(((....))).)))).--- ( -35.80)
>DroYak_CAF1 157025 113 - 1
GGAGCUGGCUCAAUUGAUGCUGACAGCGAAUGAAAGGCUGUGGCUGAGCGUCUGCAACUGGGACCAUGGCCAGAACAGUACAGCCCUGGGCACAGUGGUUGGAAAGCGAUUUG---
...(((((((((.....(((.....))).......(((((((.(((.((....))..((((........))))..)))))))))).))))).)))).(((....)))......--- ( -35.90)
>consensus
GGAGCUGGCUCAAUUGAUGCUGACAGCGAAUGAAAGGCUCUGGCUGAGAGUCUGCAACUGAGACCACGGCCAGAACGGCACAGCCCUGGGCACAGUGGUUGAAAAACGAUUUG___
.(((....)))(((((.(((((...((.........))((((((((.(.((((.......))))).)))))))).)))))((((((((....))).))))).....)))))..... (-33.94 = -33.46 +  -0.48)

alignment

secondary structure

dotplot

Window 9

Location	11,966,586 – 11,966,686
Length	100
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	92.84
Mean single sequence MFE	-38.50
Consensus MFE	-35.60
Energy contribution	-35.72
Covariance contribution	0.12
Combinations/Pair	1.09
Mean z-score	-1.21
Structure conservation index	0.92
SVM decision value	0.46
SVM RNA-class probability	0.744314
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11966586 100 - 22407834
AACAUAGCACUGGCUCAUAUAUCUUGGGUCUGAAUGGU-----UGGCCGGAGGAGCGGAGAUCUCGACGAUCUUGGGAGCCAUCGGGGCUCGGCUUUUGCGGUGU
....((((...((((((.......))))))......))-----))((((.((((((.((((((.....))))))..(((((.....))))).)))))).)))).. ( -36.70)
>DroSec_CAF1 186000 100 - 1
AACAUAGCACUGGCUCAUAUAUCUUGGGCCUGAAUGGU-----UGGCCGGAGGAGCGGAGAUCUCGCCGAUCUUGGGAGCCAUCGGGGCUCGGCUUUUGCGGUGU
....((((...((((((.......))))))......))-----))((((.((((((.((((((.....))))))..(((((.....))))).)))))).)))).. ( -39.40)
>DroSim_CAF1 152339 100 - 1
AACAUAGCACUGGCUCAUAUAUCUUGGGCCUGAAUGGU-----UGGCUGGAGGAGCGGAGAUCUCGCCGAUCUUGGGAGCCAUCGGGGCUCGGCUUUUGCGGUGU
.((((.(((..((((......((((.((((........-----.)))).))))..(.((((((.....)))))).)(((((.....)))))))))..))).)))) ( -37.40)
>DroEre_CAF1 160664 100 - 1
AACAUAGCACUGGCUCAUAUAUCUUGGGCCUGAAUGGC-----UCACCGGAGGAGCGCAGAUCCCGCAGAUCUUGGGAGCCAUCGGGGCUCGGCUUUUGCGGUGU
.....(((...((((((.......))))))......))-----)(((((.((((((..(((((.....)))))...(((((.....))))).)))))).))))). ( -39.50)
>DroYak_CAF1 157138 105 - 1
AACAUAGCACUGGCUCAUAUAUCUUGGGCCUGAAUGGUUCGGUUCGCCGGAGGAGCGCUGAUCUCCGAGAUCUUGGGAGCCAUCGGGGCUCGGCUUUUGCGGUGU
......((((((((((.....(((.(((((.....)))))((....))))).))))(((((.((((((..((....))....)))))).))))).....)))))) ( -39.50)
>consensus
AACAUAGCACUGGCUCAUAUAUCUUGGGCCUGAAUGGU_____UGGCCGGAGGAGCGGAGAUCUCGCCGAUCUUGGGAGCCAUCGGGGCUCGGCUUUUGCGGUGU
..(((..((..((((((.......)))))))).))).........((((.((((((.((((((.....))))))..(((((.....))))).)))))).)))).. (-35.60 = -35.72 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:28 2006